The International Court of Justice (ICJ) has ruled Japan must immediately stop its whaling program in the Antarctic.

The ICJ's 16-judge panel ruled 12 votes to four in favour of Australia's argument that Japan's whaling program was not in fact designed and carried out for scientific purposes.

The court ruled that Japan must revoke current whaling permits and refrain from issuing any more.

Japan has used the 1946 International Convention for the Regulation of Whaling, which permits killing for research, to justify killing whales in the Antarctic.

But the court's judges agreed with Australia that the Japanese research - two peer-reviewed papers since 2005, based on results obtained from just nine killed whales - was not proportionate to the number of animals killed.

"In light of the fact the JARPA II [research program] has been going on since 2005, and has involved the killing of about 3,600 minke whales, the scientific output to date appears limited," presiding judge Peter Tomka of Slovakia said.

"Japan shall revoke any existent authorisation, permit or licence granted in relation to JARPA II and refrain from granting any further permits in pursuance to the program."

Japan signed a 1986 moratorium on whaling, but has continued to hunt up to 850 minke whales in the icy waters of the Southern Ocean each year.

The ICJ's ruling is final and there will be no appeal.

A spokesman for the Japanese government said the court's decision was "deeply disappointing".

"We are deeply disappointed and regret that the court ruled that Japan's research whaling program in the Antarctic did not fall within the special permit clause of the treaty," spokesman Nori Shikata told ABC NewsRadio.

"However Japan will abide by the judgement of the court that places a great importance on the international legal order and the rule of law.

"We will abide by the decision of the courts and although we will consider a concrete future course of action very carefully, upon studying what is stated in the judgement, we will cease the current research whaling program in the Antarctic pursuant to the judgement.

"This is a final verdict and we are saying in a very straight forward way that we will abide by the judgement of the court."

While it has committed to abide by the court's ruling, Japan would be free to continue whaling if it withdrew from the 1986 moratorium or the 1946 treaty.

Japan had argued it had complied with the moratorium despite its 2,000-year tradition of whale hunting, leaving coastal communities in "anguish" because they can no longer practise their ancestral traditions.

Prime Minister Tony Abbott has reacted to the finding saying it was long-standing policy of both sides of politics to call for an end to Japan's whaling program.

"I very much appreciate the desire of the Australian people generally to see an end to whaling in the Southern Ocean," he said.

The decision has come less than a week before Mr Abbott is set to travel to Japan, with hopes of finalising a long-awaited free trade agreement which he has described as the Government's "absolute priority at the moment".

"I'm looking forward to my trip to Japan in a few days time, and I'm certainly looking forward to building on a very good relationship - a relationship which is certainly much, much, much bigger than any disagreement we might have had about whaling," he said.

Greens Senator Peter Whish-Wilson wants the Prime Minister to raise the issue when he is in Japan.

"We need to use whatever diplomatic means we can to ensure that the Japanese do abide by this decision," he said.

The Federal Opposition says the Government should now talk with Japan about genuine and non-lethal options for whale research.

ICJ ruling 'vindication' of Australia's legal action

Former prime minister Kevin Rudd, whose government first launched the legal action in May 2010, said he is "delighted by the result".

"It's great for these extraordinary creatures of the deep - whether they be minke whales or humpback whales or fin whales - it's all part of an important global conservation effort," he said.

His former environment minister Peter Garrett said he was overjoyed by the finding.

"This is a comprehensive and resounding decision in Australia's favour," he told the ABC.

"It means we won't see harpoons in the Southern Ocean - we certainly shouldn't see them down there any longer.

"I'm absolutely over the moon for all those people who wanted to see the charade of scientific whaling cease once and for all.

"This was a pioneering piece of litigation - the first time that there had been litigation in the International Court of Justice about an environmental treaty," he said.

"It's going to pave the way for more environmental litigation I could expect between nations."

Bob Brown hails 'whale of a win'

Greens founder and Sea Shepherd director Bob Brown declared on Twitter that the ICJ's ruling was a "whale of a win".

He said he does not expect Japan will apply for new permits to hunt whales in the Southern Ocean.

"Japan, like all other great nations, has it's reputation to think of. And I don't think it's going to put a huge money loser like this in front of its global reputation. The court ruling is a blessing in disguise for Japan," he said.

Sea Shepherd global executive officer and former captain of the Steve Irwin protest ship, Alex Cornelissen, said Australia's advocacy was an important factor in the outcome.

"It's very hard to predict how the international court is going to vote on a case like this so it was a big surprise for everybody really," he told ABC NewsRadio.

"We finally got the ultimate result and that is that no more whales will be killed in the southern ocean whale sanctuary and that's fantastic."

Don Rothwell, a professor of international law at the Australian National University, told Lateline the decision may not bring Japanese whaling in the Southern Ocean to an end.

"The court of course was not asked to strike out Article Eight of the whaling convention - that's the contentious provision which permits so-called scientific whaling," he said.

"It needs to be remembered that Article Eight of the whaling convention remains in place and Japan has the opportunity to interpret that consistently with international law."

Professor Rothwell said he would be interested to see how Japan reacts to the decision over the coming days.

"Japan has threatened that it would withdraw from the International Convention for the Regulation of Whaling and therefore withdraw from the International Whaling Commission on multiple occasions over the last decade or so," he said.

"And indeed, in the very final submissions that Japan made to the court in July last year, Japan alluded to the fact that as a result of its concerns about "cultural imperialism" - which was the way in which it sought to characterise aspects of Australia's arguments - that Japan may need to reconsider whether it would remain a party to the whaling convention."

Japan, Iceland and Norway the only remaining whaling countries

Whaling was once widespread around the world, but Japan is now one of only three countries, alongside Iceland and Norway, that continue the practice.

The meat is popular with some Japanese consumers, who consider it a delicacy.

Norway, the other main whaling nation, in 1993 shifted away from scientific whaling to "commercial" catches, where the meat is sold directly to consumers.

Norway set a quota of 1,286 minke whales in the north Atlantic in last year's summer hunt, saying stocks were plentiful in the region.

Fishermen rarely catch the full quota, partly because demand has sunk in recent years.

Iceland and Norway do not claim to be carrying out research, meaning the ICJ's ruling has no immediate consequences for them.

However, activists said the ruling reflected a gradual changing of opinion that would put an end to whaling.

More than 10,000 whales have been killed since 1988 as a result of Japan's programs.